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Links tagged with 'pubmed'

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Found 23 links

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3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint

DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology dna-binding proteins genetic databases genetic regulation humans nucleic acid databases protein conformation protein databases protein-DNA complex pubmed regulator genes sequence alignment

BioLitTool Content

http://biolit.ucsd.edu

Literature > Text Mining and Semantics

BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.

NAR Web Server Issue 2008
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tagsfactual databases protein databases pubmed systems integration

ChilibotTool Content

http://www.chilibot.net/

Literature > Text Mining and Semantics

Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.

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tagsbiology information services natural language processing protein binding protein databases pubmed software design

ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene

DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

NAR Database Issue 2010
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tagsalgorithms animals chromosomes computational biology gene expression profiling genetic databases genetic translocation humans nucleic acid databases protein databases pubmed

eTBLASTDatabase Content

http://etest.vbi.vt.edu/etblast3/

Literature > Search Tools

eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence authorship automated pattern recognition bibliographic databases controlled vocabulary database management systems humans informatics medline natural language processing peer review periodicals as topic publications publishing pubmed software design

GenoWatchTool Content

http://genepipe.ngc.sinica.edu.tw/genowatch

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

NAR Web Server Issue 2008
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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases microsatellite repeats pubmed single nucleotide polymorphism

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene

DNA > Annotations
Literature > Text Mining and Semantics

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

NAR Web Server Issue 2009
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tagsanimals bone resorption controlled vocabulary gene expression profiling genes hepatoerythropoietic porphyria humans mice mutation oligonucleotide array sequence analysis osteoporosis pancreatic neoplasms pubmed rats

GoPubMedTool Content

http://www.gopubmed.org/

Literature > Search Tools

GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.

NAR Web Server Issue 2005
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tagscontrolled vocabulary enzyme inhibitors genetic databases levamisole pubmed subject headings

HubMedTool Content

http://www.hubmed.org/

Literature > Search Tools

HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.

NAR Web Server Issue 2006
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tagspubmed systems integration

iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

NAR Web Server Issue 2007
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tagsanimals arabidopsis biology biomedical engineering caenorhabditis elegans computational biology database management systems drosophila melanogaster escherichia coli genes humans mice natural language processing periodicals as topic publications pubmed signal transduction software design zebrafish

Laminin databaseDatabase Content

http://www.lm.lncc.br

Protein > Databases

The Laminin(LM)-database is a database focusing on the non-collagenous extracellular matrix protein family, the LMs. The homepage is subdivided into LMs, receptors, extracellular binding and other related proteins. Each tab opens into a given LM or LM-related molecule, where the reader finds a series of further tabs for 'protein', 'gene structure', 'gene expression' and 'tissue distribution' and 'therapy'. Data are separated as a function of species, comprising Homo sapiens, Mus musculus and Rattus novergicus.

NAR Database Issue 2011
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tagsanimals gene expression humans laminin mice protein databases pubmed rats tissue distribution

LitInspectorTool Content

http://www.litinspector.org/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.

NAR Web Server Issue 2009
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tagsanimals humans mice pubmed rats signal transduction terminology as topic

LitMinerTool Content

http://andromeda.gsf.de/litminer

Literature > Text Mining and Semantics

LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, compounds, diseases and phenotypes, and tissues and organs.

NAR Web Server Issue 2005
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tagsgene expression regulation pubmed

NCBI ResourcesDatabase Content

http://www.ncbi.nlm.nih.gov

DNA > Databases
Expression > Databases
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > Databases
RNA > Databases

The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.

NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms animals bacterial genome computational biology dna sequence analysis gene expression genetic databases genomics humans national institutes of health (u.s.) national library of medicine (u.s.) nucleic acid databases protein databases pubmed rna sequence analysis sequence alignment systems integration tertiary protein structure united states viral genome

NLProtTool Content

http://cubic.bioc.columbia.edu/services/nlprot/index.html

Literature > Text Mining and Semantics
Protein > Sequence Retrieval

NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.

NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence artificial intelligence protein databases publications pubmed terminology as topic